Molecular Genetics
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12503/21632
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Item Mitochondrial RNA Sequencing Variation in Age-Related Pathologies(2019-03-05) Phillips, Nicole; Silzer, Talisa K.Background. Mitochondrial function has been implicated in a number of age-related disease pathologies, and post-transcriptional sequence modifications in mitochondrial RNA (mtRNA) have been correlated with variation in the mitochondrial function. One of the most significant modifications is methylation of mitochondrial transfer RNAs (tRNA) at their 9th position (termed “p9 sites”). Post-transcriptional modifications to these tRNAs are known to alter efficiency of translation and protein synthesis, affecting downstream mitochondrial function. The impact that these modifications to the mitochondrial transcriptome have on risk for age-related disease has not been previously explored. Purpose. The purpose of this study was to determine if altered post-transcriptional modification rates to mitochondrial p9 tRNA sites is associated with risk for age-related disease pathologies. Methods. RNA sequencing and genotyping data was analyzed from cerebellar tissue of 275 Caucasian subjects consisting of elderly controls, and individuals with diagnosed AD, progressive supranuclear palsy or pathological aging. Data were obtained through the Synapse data repository and were collected by the Mayo RNAseq study, led by Dr. Nilüfer Ertekin-Taner, Mayo Clinic, Jacksonville, FL as part of the multi-PI U01 AG046139 (MPIs Golde, Ertekin-Taner, Younkin, Price). Heteroplasmy in mtRNA was measured using the VarScan software tool. Variants in the nuclear-encoded gene MRPP3 were analyzed for association with altered p9 methylation rates. Results. Average number and rate of heteroplasmy at the 13 sites were compared across control and case groups. A higher rate of heteroplasmy was observed at the p9 sites, indicating the presence of methylation within these tRNAs. Concluding Remarks. Post-transcriptional modification of mtRNA occurs under normal, non-pathologic states; alteration of methylation rate at the p9 site of mitochondrial tRNAs may be associated with aging pathology. The rate of p9 methylation has been associated with genetic factors encoded in the nuclear DNA (Hodgkinson et al., 2014). Targeting methylation of mitochondrial tRNA could prove to be a viable therapeutic approach for deficits in mitochondrial function.Item Candidate Gene Association Study of Low Back Pain Using SNP Derived Gene Expression Profiling: A PRECISION PAIN Research Registry Study(2019-03-05) Pathak, Gita; Aryal, Subhash; Phillips, Nicole R.; Licciardone, John C.; Bhatnagar, ShwetaCandidate Gene Association Study of Low Back Pain Using SNP Derived Gene Expression Profiling: A PRECISION PAIN Research Registry Study Shweta Bhatnagar, Gita Pathak, Subhash Aryal, Nicole Phillips, John Licciardone Abstract Objective: The Global Burden of Disease Study estimated that 632 million persons worldwide are affected by low back pain (LBP), making it the leading cause of disability worldwide. Furthering our understanding of genetic-based risk for LBP may allow for development of targeted gene therapy for pain which may help mitigate the healthcare and financial burden. Inflammatory genes have been implicated in pain disorders. Variability in how these genes are expressed may determine their association in low back pain. This study aims to predict the expression of candidate genes and their association with pain in participants of the PRECISION Pain Research Registry. Hypothesis: Elevated self-reported pain intensity and disability from LBP is associated with the higher expression of inflammatory genes. Methods: The DNA was collected, extracted, and genotyped using the Infinium® Global Screening Array (Illumina). Data were filtered based on standard quality control protocols (Anderson et al., 2010). Gene expression data of monocytes from the Multi-Ethnic Study for Atherosclerosis (MESA) was used for gene expression imputation using PrediXcan. Twenty-six candidate genes involved with inflammation and immune response processes (based on Gene Ontology Analysis) were analyzed. The imputed gene expression levels were transformed to dichotomized gene expression levels, over-expressed and under-expressed. The highly expressed gene levels were then tested for association with PRECISION participant outcomes data, including Roland-Morris Disability Score and a pain intensity score using SPSS. Results: Seven genes showed positive correlation between their predicted expression levels and scores on the Roland-Morris Questionnaire and the pain intensity scale for LBP: STAT-1, STAT-2, HLA-A, CD48, CD209, CLEC4G and SLAMF8. Also, as expected, many of these genes demonstrated co-expression patterns due to their common role in immune mediation. Conclusions: The results demonstrate a positive correlation between the increased expression of inflammatory genes and how the subjects perceived and reported LBP. Understanding the relationship between pain and variability in inflammatory genes could play a role in future precision medicine and pain management.Item Examining SLC6A4 Variations in the PRECISION Pain Research Registry(2019-03-05) Phillips, Nicole R.; Aryal, Subhash; Licciardone, John C.; Lopez, JonathanPurpose: Chronic low back pain is the leading cause of disability globally and has been linked to comorbidities such as depression. Common pathways involving serotonin and norepinephrine may play a role in both pain and mood disorders. The SLC6A4 gene, encoding a serotonin reuptake transporter, has been heavily studied with regard to depression. Polymorphisms within the gene are thought to influence the expression of the transporter, thereby modulating serotonin transmission. More recently, this gene has been studied in the context of chronic pain. This study seeks to further our understanding of chronic pain with respect to depression and other outcome measures in participants with chronic low back pain to aid in the development of better treatments. Methods: Participants with chronic low back pain in the PRECISION Pain Research Registry provided DNA samples that were genotyped on the Infinium Global Screening Array (Illumina). Long and short length polymorphisms of the SLC6A4 gene were predicted using an eight single nucleotide polymorphism (SNP) machine learning model. Of the eight, one SNP was collected from the array, and the other seven were imputed. Additionally, the rs25531A [greater than] G SNP was imputed. Using the length of the polymorphism and the rs25531 SNP, subjects were divided into high, intermediate and low expression groups. Participants also reported clinical status measures such as low back pain intensity, back-specific functioning, PROMIS quality of life, levels of pain self-efficacy, and pain catastrophizing. Results: There was no significant association between self-reported depression and expression levels (high, intermediate, low) of SLC6A4. No correlation was found between PROMIS depression scores and SLC6A4 expression. Analyses for depression values were conducted using logistic linear regression and non-parametric ANOVA respectively. There were no observed correlations between transporter expression level and the outcome variables of back-related disability, pain, pain catastrophizing, or pain self-efficacy. Disability was analyzed using ANOVA. Pain, pain catastrophizing, and pain self-efficacy were investigated using non-parametric ANOVA analyses. Conclusion: No correlations were found between serotonin transporter expression level and depression or other outcome variables. Similar previous studies investigating SLC6A4 used homogenous populations. We recommend conducting a larger study that takes into account race.Item Mito-nuclear compatibility in risk for cognitive decline in admixed populations(2019-03-05) Pathak, Gita; Barber, Robert C.; Phillips, Nicole R.; Silzer, Talisa K.Background. The issue of missing heritability has vexed the study of many complex diseases, Alzheimer’s disease (AD) not excluded. Only ~35% of the heritability of AD has been accounted for, the majority of which lies in APOE allele e4, which has a less-pronounced effect in certain admixed populations. There are few genetic and/or mitochondrial studies of admixed populations, and our understanding of mitochondrially-related cognitive decline has largely been based on studies of highly homogenous populations (by design). The concept of mito-nuclear compatibility states that optimization of mitochondrial DNA (mtDNA) with nuclear genetic background is a source of significant selective evolutionary pressure. Evidence for this phenomenon in human populations is emerging (Zaidi and Makova, 2019), and opens the door for studies in the context of human disease. Purpose. The purpose of this study is to determine whether divergent nuclear and mitochondrial genomes confer risk for cognitive impairment and decline in admixed populations. Methods. Participants in the Texas Alzheimer’s Research and Care Consortium (TARCC) were used for this study. DNA extracts from peripheral blood buffy coat were genotyped on the Multi-Ethnic Genotyping Array (Illumina) which types 1.7 million SNPs and includes ancestry specific genetic variation. The top 10 eigenvectors (smartpca via Eigensoft) were generated via principle component analysis of nuclear DNA (nDNA) and used to cluster subjects with the 1000 Genomes population data in order to ascertain global, ancestral nDNA background. Mitochondrial DNA variants from the array were analyzed using HaploGrep/MitoTool for mtDNA haplotype assignment. Non-concordance of mtDNA:nDNA ancestry will be identified and scored as in Zaidi and Makova, 2019 and tested for association with cognitive state (normal, mild cognitive impairment, or Alzheimer’s disease) as well as cognitive decline between time points. Results. Preliminary studies indicate that cognitive decline is associated with mitochondrial phenotypes in Caucasian subjects; these results were dependent on sex. Mitochondrial copy number was a main driver in the predictive model in both males and females, but to a differing degree. Conclusion. Discrepancy between mtDNA and nDNA genomic backgrounds has been previously correlated with mtDNA copy number (Zaidi and Makova, 2019); similar discrepancy may explain health disparities in complex diseases that are more prevalent in particular admixed populations.